Question: Does .sra.cache file means failed download?
0
gravatar for Phoenix Mu
4 months ago by
Phoenix Mu0
Phoenix Mu0 wrote:

I am using fastq-dump to download some files from sra. It turned that .sra files was downloaded into my home directory. So, there was a "disk quota exceeded" error, and a number of .sra.cache instead of .sra files were generated. But, the downloading is continuing. I wonder if the fastq.gz files downloaded in this case are deprecated? Thanks

sra • 365 views
ADD COMMENTlink modified 4 months ago by Renesh1.6k • written 4 months ago by Phoenix Mu0
2
gravatar for ATpoint
4 months ago by
ATpoint15k
Germany
ATpoint15k wrote:

The cache files are downloaded by default, see e.g. here. You can (and should IMHO) disable that, see here. In any case, using fastq-dump for download is not efficient, for a suggested workflow see my answer in this thread: Method to Check Fastq Completeness after Fastq-dump

Most data are anyway backed up at the European Nucleotide Archive, where you can download them much more efficiently and directly in fastq format. See my tutorial on that matter: Fast download of FASTQ files and metadata from the European Nucleotide Archive (ENA)

ADD COMMENTlink written 4 months ago by ATpoint15k
2
gravatar for Renesh
4 months ago by
Renesh1.6k
United States
Renesh1.6k wrote:

If you see .sra.cache files under SRA directory, it means your download is not complete and got interrupted for some reason. vdb-validate command will fail for the corresponding accession. See this post for downloading SRA datasets: https://reneshbedre.github.io/blog/fqutil.html

ADD COMMENTlink written 4 months ago by Renesh1.6k
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